public override string ToString()
{
var sb = new StringBuilder("StructB(");
int tmp198 = 0;
if ((Aa != null) && __isset.aa)
{
if (0 < tmp198++)
{
sb.Append(", ");
}
sb.Append("Aa: ");
Aa.ToString(sb);
}
if ((Ab != null))
{
if (0 < tmp198)
{
sb.Append(", ");
}
sb.Append("Ab: ");
Ab.ToString(sb);
}
sb.Append(')');
return(sb.ToString());
}
/// <summary>
///
/// </summary>
/// <param name="nChain">The peptide that will be constitute the N-terminal region of the resultant spliced peptide</param>
/// <param name="cChain">The peptide that will be constitute the C-terminal region of the resultant spliced peptide</param>
/// <param name="nInclude">The included portion of the N-terminal peptide</param>
/// <param name="cInclude">The included portion of hte C-terminal peptide</param>
/// <param name="nAlignNullable">The region to align on prior to splicing</param>
/// <param name="cAlignNullable">The region to align on prior to splicing</param>
/// <returns></returns>
public static IChain GetPeptide(IChain nChain, IChain cChain, Range nInclude, Range cInclude, Range?nAlignNullable = null, Range?cAlignNullable = null)
{
bool performAlignment = nAlignNullable != null && cAlignNullable != null;
Range nAlign = performAlignment ? new Range((Range)nAlignNullable) : new Range();
Range cAlign = performAlignment ? new Range((Range)cAlignNullable) : new Range();
if (performAlignment && ((Range)nAlignNullable).Length != ((Range)cAlignNullable).Length)
{
throw new ArgumentException("Splice ranges must be of equal length");
}
if (nInclude.Start < 0 || nChain.Count <= nInclude.End || cInclude.Start < 0 || cChain.Count <= cInclude.End)
{
throw new IndexOutOfRangeException("Splice ranges exceed the peptide ranges");
}
IChain chain = new Chain();
//float rmsd = Rmsd.GetRmsd(cTerminus[cAlign.Start, cAlign.End], nTerminus[nAlign.Start, nAlign.End]);
Matrix cTerminusTransform = performAlignment ? Rmsd.GetRmsdTransform(cChain[cAlign.Start, cAlign.End], nChain[nAlign.Start, nAlign.End]) : Matrix.Identity;
cTerminusTransform.Rotation.Normalize();
//Quaternion rotation = cTerminusTransform.Rotation;
//rotation.Normalize();
//cTerminusTransform.Rotation = rotation;
for (int i = nInclude.Start; i <= nInclude.End; i++)
{
chain.Add(new Aa(nChain[i]));
}
for (int i = cInclude.Start; i <= cInclude.End; i++)
{
IAa residue = new Aa(cChain[i]);
residue.Transform(cTerminusTransform);
chain.Add(residue);
}
return(chain);
}
public void Write(TProtocol oprot)
{
oprot.IncrementRecursionDepth();
try
{
TStruct struc = new TStruct("StructB");
oprot.WriteStructBegin(struc);
TField field = new TField();
if (Aa != null && __isset.aa)
{
field.Name = "aa";
field.Type = TType.Struct;
field.ID = 1;
oprot.WriteFieldBegin(field);
Aa.Write(oprot);
oprot.WriteFieldEnd();
}
field.Name = "ab";
field.Type = TType.Struct;
field.ID = 2;
oprot.WriteFieldBegin(field);
Ab.Write(oprot);
oprot.WriteFieldEnd();
oprot.WriteFieldStop();
oprot.WriteStructEnd();
}
finally
{
oprot.DecrementRecursionDepth();
}
}
public void AA_ShouldPassAddDelayedMessageToLog_WhenBagIsDelayingFlight()
{
var timerServiceMock = new Mock <ITimerService>();
timerServiceMock.Setup(ts => ts.SimulationMultiplier).Returns(1);
var flightMock = new Mock <IFlight>();
flightMock.Setup(b => b.FlightState).Returns(FlightState.Departed);
var bagMock = new Mock <Baggage>();
bagMock.Object.Destination = typeof(BagCollector).Name;
bagMock.Object.Flight = flightMock.Object;
var bagCollector = new Mock <IChainLink>();
bagCollector.Setup(bc => bc.Destination).Returns(typeof(BagCollector).Name);
var aa = new Aa(1, Guid.NewGuid().ToString(), timerServiceMock.Object);
aa.AddSuccessor(bagCollector.Object);
aa.PassBaggage(bagMock.Object);
bagMock.Object.Log.ShouldContain(l => l.Description.Contains(LoggingConstants.BagArrivedLateAtAirportArea));
}
public void AA_ShouldPassBaggageToBagCollector_WhenBagIsForBagCollector()
{
var timerServiceMock = new Mock <ITimerService>();
timerServiceMock.Setup(ts => ts.SimulationMultiplier).Returns(1);
var flightMock = new Mock <IFlight>();
flightMock.Setup(b => b.FlightState).Returns(FlightState.InPreparation);
var bagMock = new Mock <IBaggage>();
bagMock.Setup(b => b.Destination).Returns(typeof(BagCollector).Name);
bagMock.Setup(b => b.Flight).Returns(flightMock.Object);
var bagCollector = new Mock <IChainLink>();
bagCollector.Setup(bc => bc.Destination).Returns(typeof(BagCollector).Name);
var aa = new Aa(1, Guid.NewGuid().ToString(), timerServiceMock.Object);
aa.AddSuccessor(bagCollector.Object);
aa.PassBaggage(bagMock.Object);
bagMock.Object.Destination.ShouldBe(typeof(BagCollector).Name);
}
private void button2_Click(object sender, EventArgs e)
{
Aa.Clear();
Bb.Clear();
Hh.Clear();
rez.Clear();
}
static void Main()
{
InheritanceToInterface obj = new InheritanceToInterface();
Aa obj2 = (Aa)obj;
Bb obj3 = (Bb)obj;
obj2.Add();
obj3.Add();
Console.Read();
}
static void AddDisulfides(Chain peptide)
{
for (int i = 0; i < peptide.Count - 1; i++)
{
IAa residue1 = peptide[i];
if (residue1.Name != "CYH")
{
continue;
}
for (int j = i + 1; j < peptide.Count; j++)
{
IAa residue2 = peptide[j];
if (residue2.Name != "CYH")
{
continue;
}
Vector3 SG1 = residue1["SG"].Xyz;
Vector3 SG2 = residue2["SG"].Xyz;
if (!VectorMath.IsValid(SG1) || !VectorMath.IsValid(SG2))
{
continue;
}
if (Vector3.Distance(SG1, SG2) < 2.5)
{
IAa replace1 = new Aa("CYS", residue1.IsNTerminus, residue1.IsCTerminus);
replace1.AlignToNCAC(residue1);
foreach (IAtom atom in residue1)
{
IAtom match = replace1[atom.Name];
if (match != null)
{
match.Xyz = atom.Xyz;
}
}
IAa replace2 = new Aa("CYS", residue2.IsNTerminus, residue2.IsCTerminus);
replace2.AlignToNCAC(residue2);
foreach (IAtom atom in residue2)
{
IAtom match = replace2[atom.Name];
if (match != null)
{
match.Xyz = atom.Xyz;
}
}
peptide[i, true] = replace1;
peptide[j, true] = replace2;
break;
}
}
}
}
public void TestWildCardEventInActor()
{
var config = new LogEvent();
this.Test(r =>
{
Aa.RunTest(r, config);
});
string actual = config.ToString();
Assert.True(actual is "E2,UnitEvent,E1");
}
public override int GetHashCode()
{
int hashcode = 157;
unchecked {
if ((Aa != null) && __isset.aa)
{
hashcode = (hashcode * 397) + Aa.GetHashCode();
}
if ((Ab != null))
{
hashcode = (hashcode * 397) + Ab.GetHashCode();
}
}
return(hashcode);
}
public void AA_ShouldPassBaggageToMpa_WhenBagIsForMpa()
{
var timerServiceMock = new Mock <ITimerService>();
var bagMock = new Mock <IBaggage>();
bagMock.Setup(b => b.Destination).Returns(typeof(Mpa).Name);
var mpaMock = new Mock <IChainLink>();
mpaMock.Setup(mpa => mpa.Destination).Returns(typeof(Mpa).Name);
var aa = new Aa(1, Guid.NewGuid().ToString(), timerServiceMock.Object);
aa.AddSuccessor(mpaMock.Object);
aa.PassBaggage(bagMock.Object);
bagMock.Object.Destination.ShouldBe(typeof(Mpa).Name);
}
public async global::System.Threading.Tasks.Task WriteAsync(TProtocol oprot, CancellationToken cancellationToken)
{
oprot.IncrementRecursionDepth();
try
{
var struc = new TStruct("StructB");
await oprot.WriteStructBeginAsync(struc, cancellationToken);
var field = new TField();
if ((Aa != null) && __isset.aa)
{
field.Name = "aa";
field.Type = TType.Struct;
field.ID = 1;
await oprot.WriteFieldBeginAsync(field, cancellationToken);
await Aa.WriteAsync(oprot, cancellationToken);
await oprot.WriteFieldEndAsync(cancellationToken);
}
if ((Ab != null))
{
field.Name = "ab";
field.Type = TType.Struct;
field.ID = 2;
await oprot.WriteFieldBeginAsync(field, cancellationToken);
await Ab.WriteAsync(oprot, cancellationToken);
await oprot.WriteFieldEndAsync(cancellationToken);
}
await oprot.WriteFieldStopAsync(cancellationToken);
await oprot.WriteStructEndAsync(cancellationToken);
}
finally
{
oprot.DecrementRecursionDepth();
}
}
public static void load_xx(string file_path)
{
StreamReader sr = new StreamReader(file_path);
while (!sr.EndOfStream)
{
string line = sr.ReadLine();
if (line.Trim() == "")
{
continue;
}
if (line[0] != 'L')
{
continue;
}
string[] strs = line.Split(new char[] { '=', '|' }, StringSplitOptions.RemoveEmptyEntries);
string element_name = strs[1];
string element_str = strs[2];
Config_Help.link_elements_hash[element_name] = Aa.parse_Aa_byString(element_str);
}
sr.Close();
}
public override string ToString()
{
StringBuilder __sb = new StringBuilder("StructB(");
bool __first = true;
if (Aa != null && __isset.aa)
{
if (!__first)
{
__sb.Append(", ");
}
__first = false;
__sb.Append("Aa: ");
__sb.Append(Aa == null ? "<null>" : Aa.ToString());
}
if (!__first)
{
__sb.Append(", ");
}
__sb.Append("Ab: ");
__sb.Append(Ab == null ? "<null>" : Ab.ToString());
__sb.Append(")");
return(__sb.ToString());
}
public static IChain ChainFromRecords(IEnumerable <AtomRecord> records, PdbLoadOptions loadOptions = PdbLoadOptions.Default, char?chainId = null)
{
bool wellFormatted = (loadOptions) == PdbLoadOptions.WellFormatted;
bool requireNCAC = (loadOptions & PdbLoadOptions.RequireNCAC) != 0;
bool requireNonNCAC = (loadOptions & PdbLoadOptions.RequireNonNCAC) != 0;
bool missingAtomsNaN = (loadOptions & PdbLoadOptions.MissingAtomsNaN) != 0;
IEnumerable <AtomSource> allAtoms = records.Where(record => record != null).Select(record => record.ToAtom());
IEnumerable <IGrouping <char, AtomSource> > chains = allAtoms.GroupBy(atom => atom.ChainIndex);
foreach (IGrouping <char, AtomSource> chain in chains)
{
bool chainFailed = false;
char actualChainId = chain.Key;
if (chainId != null && chainId != actualChainId)
{
continue;
}
Chain peptideQuick = new Chain();
List <IGrouping <int, AtomSource> > pdbResidues = chain.GroupBy(atom => atom.ResidueIndex).OrderBy(group => group.Key).ToList();
foreach (IGrouping <int, AtomSource> pdbResidue in pdbResidues)
{
bool nTerminus = pdbResidue == pdbResidues.First();
bool cTerminus = pdbResidue == pdbResidues.Last();
AtomSource N = pdbResidue.FirstOrDefault(atom => atom.Name == "N");
AtomSource CA = pdbResidue.FirstOrDefault(atom => atom.Name == "CA");
AtomSource C = pdbResidue.FirstOrDefault(atom => atom.Name == "C");
// Get the name and create the residue
string name3 = pdbResidue.First().ResidueName;
if (name3 == "HIS") // TODO: Is this the best way of doing this?
{
if (pdbResidue.FirstOrDefault(atom => atom.Name == "HD1" || atom.Name == "1HD") != null)
{
name3 = "HID";
}
else
{
name3 = "HIE";
}
}
// Default to non-disulfide and then replace with disulfides when CYH are nearby with nearby SG atoms
if (name3 == "CYS")
{
name3 = "CYH";
}
if (!AaTable.IsResidueNameKnown(name3))
{
// TODO: Handle ions in some way
if ((new string[] { "ZN", "HOH", "H20", "AU", "CA", "MG", "SO4" }.Contains(name3)))
{
continue;
}
Console.WriteLine("Failing on unknown residue " + name3);
chainFailed = true;
break;
}
IAa residueQuick = new Aa(name3, nTerminus, cTerminus);
// Check for existence of atoms
if (N == null || CA == null || C == null)
{
if (requireNCAC)
{
// TODO: Tracer output
chainFailed = true;
break;
}
}
else if (float.IsNaN(N.XYZ.Length()) || float.IsNaN(CA.XYZ.Length()) || float.IsNaN(C.XYZ.Length()))
{
if (requireNCAC)
{
// TODO: Tracer output
chainFailed = true;
break;
}
}
else
{
residueQuick.AlignToNCAC(N.XYZ, CA.XYZ, C.XYZ);
}
if (missingAtomsNaN)
{
// Only explicitly PDB-defined atoms have real coordinates
for (int i = 0; i < residueQuick.Count; i++)
{
residueQuick[i].Xyz = new Vector3(float.NaN, float.NaN, float.NaN);
}
}
// Method 1
//foreach(AtomQuick atomQuick in residueQuick)
//{
// AtomSource atomSource = pdbResidue.FirstOrDefault(atomPdb => atomPdb.Name == atomQuick.Name);
// // Some PDBs are formatted with hydrogens like 2HD1 instead of HD12
// AtomSource alternateAtomSource = null;
// if(atomQuick.Name.StartsWith("H") && Char.IsNumber(atomQuick.Name.Last())) {
// string alternateName = atomQuick.Name.Last() + atomQuick.Name.Substring(0, atomQuick.Name.Length - 1);
// alternateAtomSource = pdbResidue.FirstOrDefault(atomPdb => atomPdb.Name == alternateName);
// }
// if(atomSource != null)
// {
// atomQuick.XYZ = atomSource.XYZ;
// }
// else if (alternateAtomSource != null)
// {
// atomQuick.XYZ = alternateAtomSource.XYZ;
// }
// else if (!allowMissingAtoms)
// {
// // TODO ... return null?
// continue;
// }
//}
// Method 2 - explicit atom name alternatives
// First pass: initialize atom locations based on exact name-matched PDB records
List <IAtom> initializedAtoms = new List <IAtom>();
List <AtomSource> usedSourceAtoms = new List <AtomSource>();
List <IAtom> uninitializedAtoms = new List <IAtom>(residueQuick);
foreach (IAtom atomQuick in residueQuick)
{
AtomSource atomSource = pdbResidue.FirstOrDefault(atomPdb => atomPdb.Name == atomQuick.Name);
if (atomSource != null)
{
atomQuick.Xyz = atomSource.XYZ;
initializedAtoms.Add(atomQuick);
uninitializedAtoms.Remove(atomQuick);
usedSourceAtoms.Add(atomSource);
}
}
// Second pass: try to initialize any remaining atoms from PDB records corresponding to known alternative atom names. Multiple
// passes are made to try to resolve the names, moving from more to less preferred.
int alternateAtomNamesMaxCount = alternateAtomNames_.Values.Select(value => value.Count).Max();
for (int nameIndex = 0; nameIndex < alternateAtomNamesMaxCount; nameIndex++)
{
foreach (Atom atomQuick in residueQuick)
{
if (initializedAtoms.Contains(atomQuick))
{
continue;
}
List <string> alternativeAtomNames = null;
if (!alternateAtomNames_.TryGetValue(atomQuick.Name, out alternativeAtomNames))
{
continue;
}
if (alternativeAtomNames.Count <= nameIndex)
{
continue;
}
IEnumerable <AtomSource> atomSources = pdbResidue.Where(atomPdb => alternativeAtomNames[nameIndex] == atomPdb.Name);
foreach (AtomSource atomSource in atomSources)
{
if (usedSourceAtoms.Contains(atomSource))
{
continue;
}
atomQuick.Xyz = atomSource.XYZ;
initializedAtoms.Add(atomQuick);
uninitializedAtoms.Remove(atomQuick);
usedSourceAtoms.Add(atomSource);
}
}
}
if (initializedAtoms.Count != residueQuick.Count)
{
if (!requireNCAC && !requireNonNCAC)
{
continue;
}
IEnumerable <IAtom> uninitializedNCAC = uninitializedAtoms.Where(atom => atom.Name == "N" || atom.Name == "CA" || atom.Name == "C").Where(atom => float.IsNaN(atom.Xyz.Length()));
IEnumerable <IAtom> uninitializedNonNCAC = uninitializedAtoms.Where(atom => atom.Name != "N" && atom.Name != "CA" && atom.Name != "C").Where(atom => float.IsNaN(atom.Xyz.Length()));
if (requireNCAC && uninitializedNCAC.Count() > 0)
{
chainFailed = true;
break;
}
if (requireNonNCAC && uninitializedNonNCAC.Count() > 0)
{
chainFailed = true;
break;
}
//// TODO: Create trace output and move this there
//Console.WriteLine("Failed to initialize residue " + residueQuick.Name);
//foreach (AtomQuick atom in uninitializedAtoms)
//{
// Console.WriteLine(atom.Name);
//}
//chainFailed = true;
//break;
}
peptideQuick.Add(residueQuick);
}
if (!chainFailed && peptideQuick.Count > 0)
{
AddDisulfides(peptideQuick);
return(peptideQuick);
}
}
return(null);
}
public Bb(Aa a)
{
}
public AbcClosable(Aa aa)
{
_aa = aa;
}
public static IChain GetChain(IChain[] peptides, SequenceAlignment[] alignments, Selection immutableAas)
{
IChain fusion = new Chain();
// Do all pairwise analysis
for (int i = 0; i < peptides.Length - 1; i++)
{
// Determine the ranges outside of the splice
int start1 = i == 0 ? 0 : alignments[i - 1].Range2.End + 1;
int end1 = alignments[i].Range1.Start - 1;
int start2 = alignments[i].Range2.End + 1;
int end2 = i < alignments.Length - 1 ? alignments[i + 1].Range1.Start - 1 : peptides[i + 1].Count - 1;
// Add the non-overlapping region of the first peptide
if (start1 <= end1)
{
foreach (Aa aa in peptides[i][start1, end1])
{
Aa copy = new Aa(aa, i == 0 && start1 == 0, false);
copy.NodeTransform = aa.TotalTransform;
fusion.Add(copy);
}
}
// Add the alignment region, selecting either from the first or second peptide so as to minimize clashes with the sidechains that
// are for sure being kept on either side
SequenceAlignment alignment = alignments[i];
Debug.Assert(alignment.Range1.Length == alignment.Range2.Length);
for (int alignmentOffset = 0; alignmentOffset < alignment.Range1.Length; alignmentOffset++)
{
int index1 = alignment.Range1.Start + alignmentOffset;
int index2 = alignment.Range2.Start + alignmentOffset;
IAa option1 = peptides[i][index1];
IAa option2 = peptides[i + 1][index2];
bool nTerminus = i == 0 && index1 == 0;
bool cTerminus = (i == peptides.Length - 2) && (index2 == peptides[i + 1].Count - 1);
if (immutableAas.Aas.Contains(option1))
{
Aa copy = new Aa(option1, nTerminus, cTerminus);
copy.NodeTransform = option1.TotalTransform;
fusion.Add(copy);
}
else if (immutableAas.Aas.Contains(option2))
{
Aa copy = new Aa(option2, nTerminus, cTerminus);
copy.NodeTransform = option2.TotalTransform;
fusion.Add(copy);
}
else
{
if (option2.Letter == 'P' && index1 >= 4)
{
SS[] ss1 = SecondaryStructure.GetPhiPsiSS(peptides[i], 5);
bool allHelical = (ss1[index1] | ss1[index1 - 1] | ss1[index1 - 2] | ss1[index1 - 3] | ss1[index1 - 4]) == SS.Helix;
if (allHelical)
{
Aa copy = new Aa(option1, nTerminus, cTerminus);
copy.NodeTransform = option1.TotalTransform;
fusion.Add(copy);
continue;
}
}
// Otherwise, select the residue with fewer clashes
int clashCount1 = end2 >= start2? peptides[i + 1][start2, end2].Select(other => Clash.AnyContact(other, option1, Clash.ContactType.SidechainSidechainClash) ? 1 : 0).Aggregate(0, (a, b) => a + b) : 0;
int clashCount2 = end1 >= start1? peptides[i][start1, end1].Select(other => Clash.AnyContact(other, option2, Clash.ContactType.SidechainSidechainClash) ? 1 : 0).Aggregate(0, (a, b) => a + b) : 0;
if (clashCount1 <= clashCount2)
{
Aa copy = new Aa(option1, nTerminus, cTerminus);
copy.NodeTransform = option1.TotalTransform;
fusion.Add(copy);
continue;
}
if (clashCount2 < clashCount1)
{
Aa copy = new Aa(option2, nTerminus, cTerminus);
copy.NodeTransform = option2.TotalTransform;
fusion.Add(copy);
continue;
}
}
}
// Add the non-overlapping region of the last peptide
if (i == peptides.Length - 2 && start2 <= end2)
{
foreach (Aa aa in peptides[i + 1][start2, end2])
{
Aa copy = new Aa(aa, false, aa.IsCTerminus);
copy.NodeTransform = aa.TotalTransform;
fusion.Add(copy);
}
}
}
return(fusion);
}